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Bagarius yarrelli

ABSTRACT: Bagarius yarrelli overview

PROVIDER: PRJNA398972 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
		Other
	SRR5943894_1.fastq.gz	Fastqsanger.gz
	SRR5943894_2.fastq.gz	Fastqsanger.gz
	SRR8606710_subreads.fastq.gz	Fastqsanger.gz
	SRR8606711_1.fastq.gz	Fastqsanger.gz

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Whole-Genome Sequencing of the Giant Devil Catfish, Bagarius yarrelli.

Project description:As one economically important fish in the southeastern Himalayas, the giant devil catfish (Bagarius yarrelli) has been known for its extraordinarily large body size. It can grow up to 2 m, whereas the non-Bagarius sisorids only reach 10-30 cm. Another outstanding characteristic of Bagarius species is the salmonids-like reddish flesh color. Both body size and flesh color are interesting questions in science and also valuable features in aquaculture that worth of deep investigations. Bagarius species therefore are ideal materials for studying body size evolution and color depositions in fish muscles, and also potential organisms for extensive utilization in Asian freshwater aquaculture. In a combination of Illumina and PacBio sequencing technologies, we de novo assembled a 571-Mb genome for the giant devil catfish from a total of 153.4-Gb clean reads. The scaffold and contig N50 values are 3.1 and 1.6 Mb, respectively. This genome assembly was evaluated with 93.4% of Benchmarking Universal Single-Copy Orthologs completeness, 98% of transcripts coverage, and highly homologous with a chromosome-level-based genome of channel catfish (Ictalurus punctatus). We detected that 35.26% of the genome assembly is composed of repetitive elements. Employing homology, de novo, and transcriptome-based annotations, we annotated a total of 19,027 protein-coding genes for further use. In summary, we generated the first high-quality genome assembly of the giant devil catfish, which provides an important genomic resource for its future studies such as the body size and flesh color issues, and also for facilitating the conservation and utilization of this valuable catfish.

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Occurrence of 3-hydroxyretinol in the freshwater fish Bagarius bagarius and Wallago attu. Isolation and synthesis.

Project description:A new chromogen that absorbs maximally at 329 nm was frequently found in the liver oils of the freshwater fish Bagarius bagarius and Wallago attu. It was shown to be a diester of 3-hydroxyretinol. 3-Hydroxyretinol was found to be a metabolite of lutein during the biosynthesis of 3-dehydroretinol in a freshwater fish. A new method for the chemical synthesis of 3-hydroxyretinol from methyl 3-dehydroretinoate is described. The possible pathway for the conversion of lutein into 3-dehydroretinol in vivo is discussed.

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De novo transcriptome analysis of Bagarius yarrelli (Siluriformes: Sisoridae) and the search for potential SSR markers using RNA-Seq.

Project description:BackgroundThe yellow sisorid catfish (Bagarius yarrelli) is a carnivorous freshwater fish that inhabits the Honghe River, Lanchangjiang River and Nujiang River of southern China and other Southeast Asian countries. However, the publicly available genomic data for B. yarrelli are limited.Methodology and principal findingsIllumina Solexa paired-end technology produced 1,706,456 raw reads from muscle, liver and caudal fin tissues of B. yarrelli. Nearly 5 Gb of data were acquired, and de novo assembly generated 14,607 unigenes, with an N50 of 2006 bp. A total of 9093 unigenes showed significant similarities to known proteins in public databases: 4477 and 6391 of B. yarrelli unigenes were mapped to the Gene Ontology (GO) and Clusters of Orthologous Groups (COG) databases, respectively. Moreover, 9635 unigenes were assigned to 242 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. In addition, 8568 microsatellites (simple sequence repeats, SSRs) were detected, and 31 pairs of polymorphic primers were characterized using wild populations of B. yarrelli from the Nujiang River, Yunnan Province, China.Conclusion/significanceThese sequences enrich the genomic resources for B. yarrelli and will benefit future investigations into the evolutionary and biological processes of this and related Bagarius species. The SSR markers developed in this study will facilitate construction of genetic maps, investigations of genetic structures and germplasm polymorphism assessments in B. yarrelli.

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Project description:An overview of small RNAs sequences existing in seed development and contrasted with vegetative tissues of the soybean

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